Package: DAISIE 4.5.0
DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Authors:
DAISIE_4.5.0.tar.gz
DAISIE_4.5.0.zip(r-4.5)DAISIE_4.5.0.zip(r-4.4)DAISIE_4.5.0.zip(r-4.3)
DAISIE_4.5.0.tgz(r-4.5-x86_64)DAISIE_4.5.0.tgz(r-4.5-arm64)DAISIE_4.5.0.tgz(r-4.4-x86_64)DAISIE_4.5.0.tgz(r-4.4-arm64)DAISIE_4.5.0.tgz(r-4.3-x86_64)DAISIE_4.5.0.tgz(r-4.3-arm64)
DAISIE_4.5.0.tar.gz(r-4.5-noble)DAISIE_4.5.0.tar.gz(r-4.4-noble)
DAISIE_4.5.0.tgz(r-4.4-emscripten)DAISIE_4.5.0.tgz(r-4.3-emscripten)
DAISIE.pdf |DAISIE.html✨
DAISIE/json (API)
NEWS
# Install 'DAISIE' in R: |
install.packages('DAISIE', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rsetienne/daisie/issues21 issues
Pkgdown site:https://rsetienne.github.io
- Bats_GreaterAntilles - Colonization and branching times of Noctilionoid bats from the Greater Antilles.
- Biwa_datalist - Colonization and branching times of 68 fish clades.
- Galapagos_datalist - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
- Galapagos_datalist_2types - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
- Galapagos_datatable - Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.
- Macaronesia_datalist - Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all
- NewZealand_birds_datalist - Colonization and branching times of New Zealand birds.
- archipelago_data - Physical data on 41 archipelagos
- archipelagos41 - DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos
- frogs_datalist - Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
- frogs_datatable - Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.
- frogs_sim_datalist - Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalist
- islands_10reps_RAW - 1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.
- islands_1type_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data
- islands_2types_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data
- stac_table - Explanatory table on meaning and use of 'stac' settings
On CRAN:DAISIE-4.5.0(2025-02-05)
Last updated 18 days agofrom:48b6fb585f. Checks:9 OK, 2 NOTE. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Feb 05 2025 |
R-4.5-win-x86_64 | OK | Feb 05 2025 |
R-4.5-mac-x86_64 | OK | Feb 05 2025 |
R-4.5-mac-aarch64 | OK | Feb 05 2025 |
R-4.5-linux-x86_64 | OK | Feb 05 2025 |
R-4.4-win-x86_64 | NOTE | Feb 05 2025 |
R-4.4-mac-x86_64 | OK | Feb 05 2025 |
R-4.4-mac-aarch64 | OK | Feb 05 2025 |
R-4.3-win-x86_64 | NOTE | Feb 05 2025 |
R-4.3-mac-x86_64 | OK | Feb 05 2025 |
R-4.3-mac-aarch64 | OK | Feb 05 2025 |
Exports:create_area_parscreate_CS_versioncreate_hyper_parscreate_parscreate_trait_parscreate_trait_pars_2KDAISIE_abm_factorDAISIE_convertprobdistDAISIE_count_speciesDAISIE_CS_max_stepsDAISIE_dataprepDAISIE_ExpEINDAISIE_ICDAISIE_IW_num_threadsDAISIE_loglik_allDAISIE_loglik_CSDAISIE_loglik_IWDAISIE_logp0DAISIE_margprobdistDAISIE_MLDAISIE_ML_CSDAISIE_ML_IWDAISIE_MW_MLDAISIE_numcoldaisie_odeint_csdaisie_odeint_iwDAISIE_plot_age_diversityDAISIE_plot_inputDAISIE_plot_islandDAISIE_plot_simsDAISIE_probdistDAISIE_simDAISIE_sim_crDAISIE_sim_cr_shiftDAISIE_sim_MWDAISIE_sim_relaxed_rateDAISIE_sim_time_depDAISIE_sim_trait_depDAISIE_sim_trait_dep_2KDAISIE_SR_loglik_allDAISIE_SR_loglik_CSDAISIE_SR_MLDAISIE_SR_ML_CS
Dependencies:apeBHcliclusterGenerationcodacodetoolscombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigpracmaquadprogRcppRcppEigenrlangscatterplot3dSparseMsubplextensortestitvctrs
DAISIE stac values
Rendered fromstac_key.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2022-04-14
Started: 2022-04-14
DAISIE FAQs
Rendered fromDAISIE_FAQs.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2025-02-05
Started: 2025-01-30
Demo optimizing parameters
Rendered fromdemo_optimize.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2021-05-26
Started: 2019-03-19
Demo simulating islands
Rendered fromdemo_sim.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2022-04-14
Started: 2019-03-19
Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE
Rendered fromdemo_CSvsIW.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2022-04-14
Started: 2020-08-11
Citation
To cite package ‘DAISIE’ in publications use:
Etienne R, Valente L, Phillimore A, Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2025). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.5.0, , https://github.com/rsetienne/daisie.
Corresponding BibTeX entry:
@Manual{, title = {DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction}, author = {Rampal S. Etienne and Luis Valente and Albert B. Phillimore and Bart Haegeman and Joshua W. Lambert and Pedro {Santos Neves} and Shu Xie and Richèl J.C. Bilderbeek and Hanno Hildenbrandt}, year = {2025}, note = {R package version 4.5.0, }, url = {https://github.com/rsetienne/daisie}, }
Readme and manuals
DAISIE: Dynamic Assembly of Island biota through Speciation, Immigration and Extinction
Branch | ![]() |
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master |
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develop |
DAISIE is an R
package that simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.
The model can be fitted to both empirical dated phylogenies and simulated data.
- For an overview of the simulation functionality see here.
- Details and an overview of the maximum likelihood inference capabilities to estimate parameters see here.
- For details on comparing between two diversity dependence models see here.
Installing DAISIE
N.B.: MacOS users may experience issues when installing DAISIE, especially when on MacOS Big Sur. If that is you case, please see here for detailed installation instructions.
The DAISIE
package has a stable version on CRAN and a development version on GitHub.
From CRAN
From within R, do:
install.packages("DAISIE")
From GitHub
Install DAISIE
from this GitHub repository by running:
install.packages("remotes")
# remotes::install_github("rsetienne/DAISIE")
install.packages("DAISIE", repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))
Using DAISIE as a package dependency
From CRAN
To your DESCRIPTION file, add DAISIE
as any normal package.
If your package directly uses DAISIE
:
Imports:
DAISIE
If your package uses DAISIE
in its peripherals (e.g. vignettes and tests):
Suggests:
DAISIE
From GitHub
Remotes:
rsetienne/DAISIE
Support/Questions
For feature requests or bug-reports or other matters, please submit an issue.
Feature branches
-
master
: build should always pass. @rsetienne has control overdevelop
tomaster
merges. -
develop
: merge of feature branches, merge withmaster
by @rsetienne iff build passes.
Contributors
DAISIE
was originally developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore and Bart Haegeman. It is continuously maintained by members of the @tece-lab, at the University of Groningen.
References
-
Etienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058
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Valente, L., Etienne, R.S., & Phillimore, A.B. (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227
-
Valente, L., Phillimore, A.B., & Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461
-
Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026
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Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053
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Valente, L., Phillimore, A.B., & Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503
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Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058
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Valente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5
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Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914
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Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf
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Santos Neves, P.*, Lambert, J. W.*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519
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Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210
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Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006
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Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, A. A. E., Dávalos, L. M., Saville, G. I., Upham, N., Valente, L. (2023). The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3